AttributeError: 'Grid' object has no attribute 'grid'

[StefanGIT]

Hi ,
while trying to multiply two grids, i get the following error:

  File "multipipsa/multipipsa.py", line 501, in runApbs
    visualizeGrid = potentialGrid * accesibilityGrid
  File "/exports/scratch/ana3/envs/mypipsa/lib/python2.7/site-packages/gridData/core.py", line 539, in __mul__
    return Grid(self.grid * _grid(other), edges=self.edges)
AttributeError: 'Grid' object has no attribute 'grid'

The relevant code lines are:

            potentialGrid = Grid(self.__data_dir+"/"+i+".dx")
            accesibilityGrid =Grid(self.__data_dir+"/"+i+".surf.dx")
            print(potentialGrid)
            print(accesibilityGrid)
            visualizeGrid = potentialGrid * accesibilityGrid

The error happens in the multiply?

[StefanGIT]

If i do the following:

            potentialGrid = Grid()
            potentialGrid.load(self.__data_dir+"/"+i+".dx")
            accesibilityGrid =Grid()
            accesibilityGrid.load(self.__data_dir+"/"+i+"_surf.dx")
            visualizeGrid = accesibilityGrid * potentialGrid

it works. Is there an issue with the Grid(filename) constructor?

[richardjgowers]

Hey @StefanGIT this line should make loading with a filename equivalent to your two step approach, but I think it's not working.

If you do potentialGrid = Grid(str(self.__data_dir+"/"+i+".dx")) does it make a difference?

[StefanGIT]

Thanks, the str(...) works as well!

[richardjgowers]

@StefanGIT what is your self.__data_dir object in this case? A pathlib object?

[StefanGIT]

might be:
cwd=os.getcwd()
apbs = ApbsRun(dataDir=cwd+"/example/pdbs",
temp=298.15,ios=0.100, structures=ingrp+outgrp)

[orbeckst]

The whole input autodetection code

GridDataFormats/gridData/core.py

Lines 127 to 158 in 8f40542

	if type(grid) is str:
	self.load(grid)
	elif not (grid is None or edges is None):
	# set up from histogramdd-type data
	self.grid = numpy.asanyarray(grid)
	self.edges = edges
	self._update()
	elif not (grid is None or origin is None or delta is None):
	# setup from generic data
	origin = numpy.asanyarray(origin)
	delta = numpy.asanyarray(delta)
	if len(origin) != grid.ndim:
	raise TypeError(
	"Dimension of origin is not the same as grid dimension.")
	if delta.shape == () and numpy.isreal(delta):
	delta = numpy.ones(grid.ndim) * delta
	elif delta.ndim > 1:
	raise NotImplementedError(
	"Non-rectangular grids are not supported.")
	elif len(delta) != grid.ndim:
	raise TypeError("delta should be scalar or array-like of"
	"len(grid.ndim)")
	# note that origin is CENTER so edges must be shifted by -0.5*delta
	self.edges = [origin[dim] +
	(numpy.arange(m + 1) - 0.5) * delta[dim]
	for dim, m in enumerate(grid.shape)]
	self.grid = numpy.asanyarray(grid)
	self._update()
	else:
	# empty, must manually populate with load()
	# print "Setting up empty grid object. Use Grid.load(filename)."
	pass

is pretty fragile and could do with a rework. At a minimum, we should not pass silently...